Don't be alarmed but you now have a big issue. The eggs she is on are not going to hatch normally. Once a bird starts sitting on a fertilized egg it will start developing. If I'm reading it right, your issue is that you are going to have chicks hatching at different days as they started developing on different days. You have more than one laying because they stop laying when they sit on eggs. That is the primary reason they need isolated.
If the clutch gets to big, the earliest eggs may not develop or will take more than 21 days. In your case, isolate her tonight and don't let another in until she hatches; candle at day 10 and pull those that aren't developing. You're going to have a staggered hatch. Hope for the best.
As for the rooster, he'll be fine as long as you let him live. He's doing his job by protecting his girls and I suspect he'll be good to the chicks. A good momma will protect them, he WILL know to leave them alone.